The Confession (Story Mission)
Keep raising a ruckus around Holland Valley, and you'll be marked again.
As before, you just have to go with it. Let yourself be captured, and endure John's gum-flapping until he asks for volunteers to be gruesomely tortured. Save some time and earn a few moral brownie points by saying 'Yes,' immediately.
He'll wheel out Hudson, leaving you some alone time. Just wheel yourself forward until you tumble down the stairs, which breaks your restraints, and officially starts the mission.
Pop back up to the room you just left to grab a pipe, and a medkit.
Go back downstairs and duck under the pipe to reach a small hatch.
Once inside, drop down to the lower level.
This will take you to a sort of cult family room. You'll automatically snag a throwing knife as you come in. Use that and/or melee & takedown attacks to dispose of the two cultists that tend to hang out here (throwing and immediately recovering a knife is very useful tactic for most of this mission).
Up the metal stairs in this room is a medkit and smoke grenade.
Return downstairs and proceed south into the 'Silo A' section. Stalk and take down the cargo wranglers there. There should be just two, but one of them has a pistol.
Go to the north end of the tunnel and turn left (west) for an entry into Silo B.
There will be a conversation going on to your left as you enter. Wait for it to break up, if you want to take a stealthy approach here.
Keep going down that same tunnel. You may encounter another guard or two, but the tunnel sectioning and offshoots make them relatively easy to ambush.
Do note the 'Exit' door on your left (south). It's locked now, but you'll be back here later.
Toward the end of the tunnel, note a locked door ahead, and another family-type room to your right.
The door can be picked open for some supplies and a revolver , or the key is in the family room by the tv (along with three or so cultists).
You don't need to kill everyone on this level, but it helps. After you've killed about half of them, a plot marker suddenly appears on your HUD, indicating the locked exit from before is now open. Follow your marker back there.
A cutscene with Hudson and John ensues, then you have 90 seconds to exit the bunker.
This about three times as many seconds as you need, so you may want to spare a moment or two to headshot the hostiles you encounter.
The reason you might want to do this is that your exit point is a chaotic mob of enemies. Rather than rushing right out to get torn apart, you can linger just inside the door, and take them out one by one.
Use bullets and/or your smoke grenades to clear a path out, and start sprinting for the plot-marked bridge.
Reach it to complete the mission.